pycytominer
Table of Contents
pycytominer is the core Python package in the Cytomining ecosystem. It provides a clean, composable API for processing single-cell morphological profiles produced by tools like CellProfiler.
Key capabilities:
- Aggregate single-cell data to well- or treatment-level profiles
- Annotate profiles with experimental metadata
- Normalize features using population-level statistics
- Select high-quality features and remove noise
- Output analysis-ready profiles in standard formats
Publication #
Nature Methods · 2025
Reproducible image-based profiling with Pycytominer
Serrano E, Chandrasekaran SN, Bunten D, Brewer KI, Tomkinson J, et al.